Mothers of children with congenital anomalies (CA) have many unique challenges during the process of treatment and concern to meet the needs of their hospitalized children. Aim: the aim of the current study was to assess the needs and challenges as perceived by mothers and their hospitalized children having congenital anomalies. Design: a descriptive exploratory research design was utilized to fit the aim of the current study. Setting: the study was conducted in the pediatric surgical ward in Cairo University Specialized Pediatric Hospital (CUSPH). Sample: A purposive sample of 100 mothers and their children with congenital anomalies participated in the current study. Data collection tools: data was collected using the following tools: A structured interview questionnaire, parent needs scale, children needs questionnaire and children challenges questionnaire. Results: the results revealed that, higher mean score of needs for mothers and their children such as emotional support; communication with medical team, participation in child care, mothers closeness, nutrition, learning and guidance. Higher mean score of challenges for mothers and their children such as health team communication, family acceptance, social stigma, poor mothers bonding, parent stress and financial responsibility. There were statistically significant correlations between mothers' challenges and their ages, place of residence and educational level, such as knowledge about surgical management, poor mothers bonding, parent stress, stigma, financial challenges and family acceptance. There were statistical significant correlations between children needs such as learning, child and mother closeness, support and guidance with their ages. Conclusion: the study findings of the current study presented higher levels of mother's needs and challenges with their children having congenital anomalies. Recommendation: Empowerment programs and supportive care for mothers and their children with congenital anomalies are mandatory.